Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle

doi:10.1016/S2095-3119(20)63261-0

摘要/Abstract

摘要：

猪是全球重要的家养动物，以骨骼肌的形式为人类重提供蛋白质。为了研究长链基因间非编码RNA（LincRNA）在猪骨骼肌发育中的功能，我们收集猪胚胎发育期间背最长肌（LDM）的RNA-seq数据，并坚定了739条lincRNA转录本，这些转录本分布在除Y染色体外的所有染色体上。然后我们对鉴定的lincRNA的分子特征进行分析，相比于蛋白编码基因，lincRNA具有较短的转录本长度、较长的外显子长度、较少的外显子数目及较高的组织特异性。除此之外，我们还对lincRNA在5个胚胎发育时期的表达丰度进行分析，鉴定了45个差异表达的lincRNA，其中有3个差异表达的lincRNA在不同的胚胎发育期均差异表达。最后我们对lincRNa的潜在靶基因进行预测，共鉴定了1537个顺式作用的靶基因及8571个反式作用的靶基因。结合上述结果我们鉴定了两个参与骨骼肌发育的关键候选lincRNA：XLOC_024652和XLOC_001832。本研究在全基因组水平鉴定猪胚胎期骨骼肌发育过程中可能涉及的lincRNA，为进一步研究lincRNa的功能及猪的遗传育种提供有价值的素材。

Abstract:

Pigs are globally farmed animals which provide protein for human consumption in the form of skeletal muscle. To better understand the function of long intergenic noncoding RNAs (lincRNAs) in porcine skeletal muscle growth and development, we collected RNA-seq data from porcine longissimus dorsi muscle (LDM) during embryonic development. We identified a total of 739 lincRNA transcripts, which were distributed on all chromosomes except the chromosome Y, and analyzed their molecular characteristics. Compared to protein-coding genes, lincRNAs showed shorter transcripts, longer exons, fewer exons and higher tissue specificity. In addition, the abundance of lincRNAs in five embryonic development stages were analyzed and 45 differentially expressed lincRNAs were screened, three of which were highly expressed in LDM during porcine embryonic development. Finally, we predicted the potential target genes and functions of the lincRNAs, and identified 1 537 cis-target genes and 8 571 trans-target genes. Furthermore, we identified two key candidate lincRNAs involved in muscle development, XLOC_024652 and XLOC_001832, for post-trial validation. Our results provide a genome-wide resource of lincRNAs which are potentially involved in porcine embryonic skeletal muscle development and lay a foundation for the further study of their functions.

Key words: lincRNAs , pig , skeletal muscle , embryo , potential target genes

. [J]. Journal of Integrative Agriculture, 2021, 20(1): 201-211.

LI Cen-cen, YU Shu-long, REN Hai-feng, WU Wei, WANG Ya-ling, HAN Qiu, XU Hai-xia, XU Yong-jie, ZHANG Peng-peng. Identification and functional prediction of long intergenic noncoding RNAs in fetal porcine longissimus dorsi muscle[J]. Journal of Integrative Agriculture, 2021, 20(1): 201-211.

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